Former Scottish international athlete Ken McEwan, now a district development officer for rugby in Glasgow, believes traditional team sports such as rugby, football and netball are missing out.
McEwan, who formerly taught at Lenzie Academy, realises his views are controversial but blames coeducational policy. "Because of that and the imbalance of staff ratios (with more women than men) in PE departments there is a tendency to restrict what they can offer.
"They choose hockey, for example, because it is suitable for mixed classes, and S3, S4 and Standard grade generally have to be coed so rugby is being dropped and even football."
McEwan, who is working closely on a major project linking Cartha Queen's Park with Holyrood Secondary School in Glasgow, says another stumbling block to the development of schools rugby in Glasgow is the lack of facilities. "There are lots of blaes pitches but very little grass," he points out.
That is one of the reasons why rugby is developing schools links with clubs. "At least there is a route through the club system but not enough clubs have youth or junior sections," McEwan says.
Political and cultural reasons can affect what subjects are offered, as could be seen from the recent debate in Plockton when it was discovered that shinty, a traditional team sport if ever there was one, had been excluded.
Charles Raeburn, chairman of Scottish Schools Sports, has much sympathy with hard-pressed PE departments. "Staff try to take on board culturally significant activities but they have to decide what time and expertise they have and put it all together and at the end of the day the amount of time available is ridiculously small."
One sport which 20 years ago had high hopes of being included in the curriculum was judo. "The cutbacks in the 1970s killed it. They did away with all the outside coaches and peripatetic teachers," Scottish Judo Federation director Colin McIver laments. "At that time we had two judo coaches employed in Edinburgh schools and there was an Edinburgh schools association.
"We have been unable to convince the colleges that judo would be something worth while. There is a judo element in teacher training but it is never more than an eight-week block."
McIver warns: "If there are no kits and the kids have to learn on coconut mats with no proper instructors they can be put off altogether and, if that is the case, we would rather encourage them to go to the clubs."
Judo's big hope now is that it will be included in the Team Sport programme next time round after just missing out when the programme was expanded to include athletics and swimming.